Research workbench
Crystal structure of YTHDC1 with fragment 4 (DHU_DC1_158)
Analyse Crystal structure of YTHDC1 with fragment 4 (DHU_DC1_158) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SZ3
- Type
- protein
- Length
- 321 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing protein 1
- UniProt
- Q96MU7
- Ligands
- M1H, SO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yth domain-containing protein 1 | protein | 157 | 34% helix, 26% strand | Q96MU7 |
| B | Yth domain-containing protein 1 | protein | 164 | 33% helix, 26% strand | Q96MU7 |
Ligands and binding sites
- M1H · ~{N}-methyl-5,6,7,8-tetrahydroquinolin-4-amine · ligand · 2 copies · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.58 | 0.79 | 31 | M1H |
| 2 | 79 | 0.44 | 0.80 | 17 | empty |
| 3 | 85 | 0.44 | 0.79 | 16 | empty |
| 4 | 99 | 0.43 | 0.78 | 15 | empty |
| 5 | 110 | 0.42 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 304 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6SZ3 · Crystal structure of YTHDC1 with fragment 4 (DHU_DC1_158) · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q96MU7
- Elsewhere: RCSB PDB 6SZ3 · PDBe 6SZ3 · UniProt Q96MU7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.